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TranscriptomicsTranscription start site mapping of Saccharomyces cerevisiae grown in YPD media using the nAnTi-iCAGE protocol
We used nAnT-iCAGE – unbiased single-nucleotide resolution method for genome-wide transcription start site (TSS) capture, to produce libraries from Saccharomyces cerevisiae total RNA. Our goal was to investigate S. cerevisiae core-promoters and assess the rules of transcription initiation in BY4741 ...
ORGANISM(S): Saccharomyces cerevisiae S288c 
2022-02-01 | E-MTAB-7465 | biostudies-arrayexpress
TranscriptomicsSLIC-CAGE (Super-Low Input Carrier-CAGE) transcription start site mapping of mouse migratory and gonadal primordial germ cells, postnatal oocytes and early embryo
We used SLIC-CAGE to map transcription start sites (TSSs) of mouse primordial germ cells from embryonic days 9.5-16.5, postnatal oocytes (P6, P14 and MII), and early 2-cell and 4-cell mouse embryos. We use this TSS data to show that the mouse germline development starts with the somatic promoter co...
ORGANISM(S): Mus musculus 
2022-02-14 | E-MTAB-9757 | biostudies-arrayexpress
TranscriptomicsSLIC-CAGE (Super-Low Input Carrier-CAGE) application on mouse primordial germ cells isolated from embryonic day E11.5
We developed SLIC-CAGE (Super-Low Input Carrier-CAGE) approach to capture 5'end of RNA polymerase II transcripts from as little as 5-10 ng of total RNA. The dramatic increase in sensitivity compared to existing CAGE methods is achieved by specially designed, selectively degradable carrier RNA. We ap...
ORGANISM(S): Mus musculus 
2018-10-25 | E-MTAB-7056 | biostudies-arrayexpress
TranscriptomicsSLIC-CAGE (Super-Low Input Carrier-CAGE) development: comparison with Saccharomyces cerevisiae nAnTi-CAGE and nanoCAGE libraries and validation of SLIC-CAGE on Mus musculus total RNA
We developed SLIC-CAGE (Super-Low Input Carrier-CAGE) approach to capture 5'end of RNA polymerase II transcripts from as little as 5-10 ng of total RNA. The dramatic increase in sensitivity compared to existing CAGE methods is achieved by specially designed, selectively degradable carrier RNA. We t...
ORGANISM(S): Saccharomyces cerevisiae S288C 
2018-10-25 | E-MTAB-6519 | biostudies-arrayexpress
TranscriptomicsCAGE experiment of S. Cerevisiae strain CEN.PK113-7D in four different chemostat conditions
The CAGE experiment was performed in four different chemostat conditions to assess if and how much the Transcription start site landscape changes in the industrial relevant S. Cerevisiae strain CEN.PK113-7D in different conditions. CAGE was also used to obtain accurate TSS annotations for each expre...
ORGANISM(S): Saccharomyces cerevisiae 
2019-01-03 | E-MTAB-6650 | biostudies-arrayexpress
TranscriptomicsCAGE-seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics (e.g. fast - green vs slow - red)
The core-promoter, a stretch of DNA surrounding the transcription-start-site (TSS), is a major integration-point for regulatory-signals controlling gene-transcription. Cellular-differentiation is marked by divergence in transcriptional-repertoire and cell- cycling behaviour between cells of differen...
ORGANISM(S): Danio rerio 
2020-06-19 | E-MTAB-8795 | biostudies-arrayexpress
TranscriptomicsNuclear SLIC-CAGE of human cortical neurons from Cornelia de Lange Syndrome patients and control individuals
We used SLIC-CAGE to map transcriptional start sites in cortical neurons from Cornelia de Lange Syndrome (CdLS) patients and control individuals. SLIC-CAGE was performed using nuclear RNA isolated from pre-frontal cortical grey matter. Usage of nuclear RNA allows enrichment of unstable RNAs, such as...
ORGANISM(S): Homo sapiens 
2021-02-27 | E-MTAB-9045 | biostudies-arrayexpress
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